scholarly journals The Aphelenchus avenae genome highlights evolutionary adaptation to desiccation

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xuehua Wan ◽  
Jennifer A. Saito ◽  
Shaobin Hou ◽  
Scott M. Geib ◽  
Anton Yuryev ◽  
...  
Keyword(s):  
Water Loss ◽  
Intrinsically Disordered Proteins ◽  
Early Stage ◽  
Body Water ◽  
Disordered Proteins ◽  
Gene Duplications ◽  
Intrinsically Disordered ◽  
Genome Wide ◽  
Aphelenchus Avenae ◽  
Species Specific

AbstractSome organisms can withstand complete body water loss (losing up to 99% of body water) and stay in ametabolic state for decades until rehydration, which is known as anhydrobiosis. Few multicellular eukaryotes on their adult stage can withstand life without water. We still have an incomplete understanding of the mechanism for metazoan survival of anhydrobiosis. Here we report the 255-Mb genome of Aphelenchus avenae, which can endure relative zero humidity for years. Gene duplications arose genome-wide and contributed to the expansion and diversification of 763 kinases, which represents the second largest metazoan kinome to date. Transcriptome analyses of ametabolic state of A. avenae indicate the elevation of ATP level for global recycling of macromolecules and enhancement of autophagy in the early stage of anhydrobiosis. We catalogue 74 species-specific intrinsically disordered proteins, which may facilitate A. avenae to survive through desiccation stress. Our findings refine a molecular basis evolving for survival in extreme water loss and open the way for discovering new anti-desiccation strategies.

scholarly journals Desiccation tolerance: an unusual window into stress biology

2019 ◽  
Vol 30 (6) ◽  
pp. 737-741 ◽  
Author(s):  
Douglas Koshland ◽  
Hugo Tapia
Keyword(s):  
Water Loss ◽  
Desiccation Tolerance ◽  
Intrinsically Disordered Proteins ◽  
Membrane Integrity ◽  
Disordered Proteins ◽  
In Vivo Studies ◽  
Intrinsically Disordered ◽  
As Stress

Climate change has accentuated the importance of understanding how organisms respond to stresses imposed by changes to their environment, like water availability. Unusual organisms, called anhydrobiotes, can survive loss of almost all intracellular water. Desiccation tolerance of anhydrobiotes provides an unusual window to study the stresses and stress response imposed by water loss. Because of the myriad of stresses that could be induced by water loss, desiccation tolerance seemed likely to require many established stress effectors. The sugar trehalose and hydrophilins (small intrinsically disordered proteins) had also been proposed as stress effectors against desiccation because they were found in nearly all anhydrobiotes, and could mitigate desiccation-induced damage to model proteins and membranes in vitro. Here, we summarize in vivo studies of desiccation tolerance in worms, yeast, and tardigrades. These studies demonstrate the remarkable potency of trehalose and a subset of hydrophilins as the major stress effectors of desiccation tolerance. They act, at least in part, by limiting in vivo protein aggregation and loss of membrane integrity. The apparent specialization of individual hydrophilins for desiccation tolerance suggests that other hydrophilins may have distinct roles in mitigating additional cellular stresses, thereby defining a potentially new functionally diverse set of stress effectors.

Sequence Specificity Despite Intrinsic Disorder: How a Disease-Associated Val/Met Polymorphism Shifts Tertiary Interactions in a Long Disordered Protein

2019 ◽  
Author(s):  
Ruchi Lohia ◽  
Reza Salari ◽  
Grace Brannigan
Keyword(s):  
Secondary Structure ◽  
Electrostatic Interactions ◽  
Intrinsically Disordered Proteins ◽  
Disordered Proteins ◽  
Sequence Specificity ◽  
Intrinsically Disordered ◽  
Specific Effects ◽  
Heterogeneous Polymer ◽  
Non Local ◽  
Dynamics Simulations

<div>The role of electrostatic interactions and mutations that change charge states in intrinsically disordered proteins (IDPs) is well-established, but many disease-associated mutations in IDPs are charge-neutral. The Val66Met single nucleotide polymorphism (SNP) encodes a hydrophobic-to-hydrophobic mutation at the midpoint of the prodomain of precursor brain-derived neurotrophic factor (BDNF), one of the earliest SNPs to be associated with neuropsychiatric disorders, for which the underlying molecular mechanism is unknown. Here we report on over 250 μs of fully-atomistic, explicit solvent, temperature replica exchange molecular dynamics simulations of the 91 residue BDNF prodomain, for both the V66 and M66 sequence.</div><div>The simulations were able to correctly reproduce the location of both local and non-local secondary changes due to the Val66Met mutation when compared with NMR spectroscopy. We find that the local structure change is mediated via entropic and sequence specific effects. We show that the highly disordered prodomain can be meaningfully divided into domains based on sequence alone. Monte Carlo simulations of a self-excluding heterogeneous polymer, with monomers representing each domain, suggest the sequence would be effectively segmented by the long, highly disordered polyampholyte near the sequence midpoint. This is qualitatively consistent with observed interdomain contacts within the BDNF prodomain, although contacts between the two segments are enriched relative to the self-excluding polymer. The Val66Met mutation increases interactions across the boundary between the two segments, due in part to a specific Met-Met interaction with a Methionine in the other segment. This effect propagates to cause the non-local change in secondary structure around the second methionine, previously observed in NMR. The effect is not mediated simply via changes in inter-domain contacts but is also dependent on secondary structure formation around residue 66, indicating a mechanism for secondary structure coupling in disordered proteins. </div>

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